If you have all the outfits and extra's unlocked it is the Manor glitch, it will not affect the game. If you did not complete the Manor in one go you will often get the 99% complete problem, if you check the PDA for the Manor likely your main objective will not be marked as complete, even though you did everything. Sometimes replaying one of the levels helps, but it has been that long l cannot remember how to get rid of it, sorry.
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